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We have calculated the structures, the heats of hydrogenation and the resonance energies of benzene isomers. All structures and energies were calculated by using the MMX force fields. Using PC model, the calculated structure parameters of benzene's 8 isomers are generally in good agreements with the experimental data. The heats of hydrogenation and resonance energy of benzene isomers are parallel to those experimental data and need a systematic adjustment of 4.5 kJ/mol.

Using a Morse type pair potential, molecular-dynamics simulations have been performed to investigate the atomic geometries, growing patterns, structural stabilities, energetics and magic sizes of Ti_n, V_n and Cr_n (n = 2-50) clusters. Following rearrangement collision of the atom–cluster system in fusion process, and absorbing their energies step by step down to 0 K, possible optimal equilibrium geometries of the clusters have been generated to tackle the structural determination problem. This approach serves an efficient alternative to the growing path identification and the optimization techniques. It has been found that titanium, vanadium and chromium clusters prefer to form three-dimensional compact structures in the determined configurations and the appearances of medium sizes are, in general, five-fold symmetry on the spherical clusters. Moreover, relevant relations between atomic arrangements in the clusters and the magic sizes have been observed.

New species with molecular formula Si₂NS, not yet observed experimentally, are described theoretically for the first time. Various levels of calculations are applied to obtain the structures, energies, dipole moments, vibrational spectra, rotational constants, and isomerization of Si₂NS species. A total of 15 minima which are connected by 21 interconversion transition states on the potential energy surface are located at the DFT/B3LYP/6-311G(d) level of theory. And at the higher (single point) CCSD(T)/6-311+G(2d)//QCISD/6-311G(2d)+ZPVE level of theory, the global state of 1 (at 0.0 kcal/mol) corresponds to a nonlinear SiNSiS with a ²A′ electronic state. The next most stable isomer of 2 (only 3.7 kcal/mol higher 1) possesses a rhomboidal-type structure similar to the global state of Si₂NO. This is followed by another local minimum of 6 (at 43.8 kcal/mol above 1) which is a nonlinear SiNSSi form with a ²A′ electronic state. Note that both 1 and 6 have the important Si≡N triple bonding. Too, the analog of (NCCS) NSiSiS is unstable due to the higher energy of its own. The bonding natures of the relevant species are also discussed. An analysis of the bonding properties and structural similarities and differences between C₂NO, C₂NS, SiCNO, and Si₂NO is also carried out.

The formation mechanisms of pentafulvenone and azafulvenone were extensively investigated at the B3LYP/6-311++G** level and the potential energy surfaces were drawn out. Ketene pentafulvenone (A) and 3-carbonyl-3H-pyrrole (C) can be formed by eliminating N₂ from the diazo ketone via α elimination reaction and ketene 2-carbonyl-2H-pyrrole (B), 4-carbonyl-4H-imidazole (D), and 2-carbonyl-2H-imidazole (E) were formed by the elimination of water or methanol from pyrrole-2-carboxylic acid (rB) and carboxylate (rD and rE) via β elimination reaction. The structures of these monomers were compared and showed some information about the bond changed characters. The structure investigation indicated that the C=C bond is activated when the nitrogen atom locates in the ortho position of the C=C=O part, and therefore ortho-monomers are more facile to react. The difference of the amount and stability of the corresponding dimers are caused by differing the position and number of nitrogen atom and the variety of the ortho-dimer is complicated. In addition, the infrared spectra of the title species were also analyzed including the vibrational frequencies, IR relative intensities, and vibrational mode assignment.

Detailed comparative analysis of properties of the tert-butyl radical and cation is performed using 14 density functional (DFT) methods combined with double-zeta and triple-zeta quality Gaussian basis sets with polarization and diffuse functions. Stability of different conformers is discussed. Structural parameters, dipole moment, adiabatic ionization potential (IP), inversion barrier and isotropic hyperfine coupling constants are examined and compared to values obtained at the standard MP2 level and to experimental data available. All methods indicate that that the CC bond in the radical is longer than in the cation by about 0.033 Å. The IP values are found to be very sensitive to the method used and range from 612 to 709 kJ/mol, but majority oscillate around 646÷656 kJ/mol. Calculated inversion barrier for the radical is higher than the experimental estimate of 2.68 kJ/mol; with the 6-311++G** basis set and most DFT methods it is predicted in the range 3.86÷4.82 kJ/mol. All DFT methods predict for the out-of-plane CC3 bending mode of the radical the frequency around 260 cm^-1, while in the cation the corresponding frequency is higher by about 180 cm^-1.

The structures and stabilities of charged, copper-doped, small silicon clusters (n = 1–7) have been systematically investigated using the density functional theory method at the B3LYP/6-311+G* level. For comparison, the geometries of neutral CuSi_n clusters were also optimized at the same level, although most of them have been reported previously [see Xiao CY, Abraham A, Quinn R, Hagelberg F, Comparative study on the interaction of scandium and copper atoms with small silicon clusters, J Phys Chem A106:11380, 2002; Liu X, Zhao GF, Guo LJ, Wang XW, Zhang J, Jing Q, Luo YH, First-principle studies of the geometries and electronic properties of Cu_mSi_n (2 ≤ m + n ≤ 7) clusters, Chin Phys16:3359, 2007]. Our results for the ground state structures of neutral CuSi_n clusters agree well with those of Liu et al. and Xiao et al. except for CuSi₃ and CuSi₇. Removing or adding an electron greatly changes some ground state structures, i.e. for , , , , and ; others are almost unchanged, e.g. , , , , . The ground states of ionic are all singlet, except for the smaller CuSi^- and . Based on the optimized geometries, various energetic properties, including binding energies, second-order difference energies, the highest occupied molecular orbit and the lowest unoccupied molecular orbital (HOMO–LUMO) energy gaps, ionization potential and electron affinities, were calculated for the most stable isomers of . All the results indicate that anionic and cationic clusters are relatively stable. The higher stability of the latter has been confirmed by Beck's observations.

The geometries, vibrational frequencies, electronic properties and reactivity of potassium supported on SBA-15 have been theoretically investigated by the density functional theory (DFT) method. The structural model of the potassium supported on SBA-15 was constructed based on our previous work [Wang ZX, Wang DX, Zhao Z, Chen Y, Lan J, A DFT study of the structural units in SBA-15 mesoporous molecular sieve, Comput. Theor. Chem.963, 403, 2011]. This paper is the extension of our previous work. The most favored location of potassium atom was obtained by the calculation of substitution energy. The calculated vibrational frequencies of K/SBA-15 are in good agreement with the experimental results. By analyzing the properties of electronic structure, we found that the O atom of Si-O(2)-K group acts as the Lewis base center and the K atom acts as the Lewis acid center. The reactivity of K/SBA-15 was investigated by calculating the activation of oxygen molecule. The oxygen molecule can be activated by K/SBA-15 with an energy barrier of 103.2 kJ/mol. In the final state, the activated oxygen atoms become new Lewis acid centers, which are predicted to act as the active sites in the catalytic reactions. This study provides a deep insight into the properties of supported potassium catalysts and offers fundamental information for further research.

In the past decade, there has been an extensive advancement in the creation of methods for the design and prediction of protein structures. Expeditious growth in protein structure and sequence databases has charged the development of computational approaches for the prediction of structures. This review focuses on fragment-based strategy, a computational approach for the prediction of the three-dimensional structure of proteins. Fragment assembly has immensely improved protein structure prediction accuracy, especially of the single-domain proteins at the fold level. Fragment libraries are generated using the dihedral angles along with local structural information of known protein structures. This leads to the construction of a full-length polypeptide chain of a query protein using the fragments present in these libraries. The energy function of the proteins is minimized contributing to multiple conformations considering the backbone atoms and “centroid” side-chain pseudo-atoms using conformational sampling. Lastly, Monte Carlo simulation is performed for the sampling of the side-chain rotamers and reduction of energy for more precise and refined model construction. The quality of the fragments determines whether the native-like conformations generated are accurate or not. The future direction as well as tools like ROSETTA, QUARK, FRAGFOLD, M-TASSER, and AlphaFold2 that use fragment assembly for optimal structure prediction have also been described and compared in this review.

Thanks to the tremendous progress in data, computing power and algorithms, AI-based material mining and design have gained much attention. However, building high-performance AI models requires efficient material structure representation. In this work, we propose a structural characterization method based on the neighborhood path complex for the first time. Specifically, we use persistent neighborhood path homology to obtain the structural features by introducing a filtration. This approach preserves more elemental information, as well as the corresponding physicochemical information, through the directed edges of the neighborhood digraph. To validate our model, we perform cross-validation with the carborane structures. The Pearson coefficient for stability prediction is as high as 0.903, which is a 15.5% improvement compared to the traditional persistent homology method. In addition, we constructed a prediction model based on the neighborhood path complex, and the Pearson coefficients for the prediction of carboranes’ HOMO, LUMO, and HOMO–LUMO gaps were 0.915, 0.946, and 0.941, respectively. The results show that our proposed method can effectively extract structural information and achieve accurate material property prediction.

Magnitude, similar to concepts like volume, cardinality or Euler characteristic, has become a key focus in combinatorics and topology. Recent advancements in topological data analysis and persistent homology have emphasized its importance. Persistent magnitude, a newly highlighted invariant introduced by Govc and Hepworth, has emerged as a notable subject of interest. In this work, we apply persistent magnitude to analyze and predict the stability of closo-carborane structures. First, we assess the stability of carboranes by employing cross-validation with different magnitude features. The Pearson correlation coefficients for stability predictions using three distinct magnitude features are 0.900, 0.882 and 0.883, respectively. These results are comparable to the Pearson correlation coefficient of 0.881 obtained when using a single feature based on persistent homology. Second, the utilization of magnitude features to predict the HOMO, LUMO and HOMO–LUMO gaps of carboranes involves conducting eight gradient boosting regressions for each scenario. The lowest correlation coefficients observed are 0.9056, 0.9385 and 0.9427, respectively. These findings highlight the promising performance of persistent magnitude features in the analysis of material structure and stability.